relax SVN archive

Created the pipe_control.mol_res_spin.count_max_spins_per_residue() function.

This will be used by the plotting module to determine if more than one spin per residue exists.

The grace.write user function data type argument sequence values have changed.

Instead of 'spin', this can now be 'res_num' or 'spin_num' to specify that either the residue number
or spin number should be plotted on the desired axis. The x_data_type now defaults to 'res_num'.

Created the pipe_control.plotting module.

This will be used as a base for the plotting of all types of data. This includes the current OpenDX
and Grace modules, as well as future modules. The determine_functions() function has been added and
is used to simplify the pipe_control.grace.get_data() function.

Merged revisions 19399 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r19399 | bugman | 2013-04-05 19:57:42 +0200 (Fri, 05 Apr 2013) | 7 lines

The common spin methods of the specific analysis API now ignore parameters not in the model.

This affects the _data_init_spin(), _sim_init_values_spin(), and _sim_return_param_spin() methods.
The result is that the spin containers no longer hold parameter variables set to None for non-model
parameters.
........

The common spin methods of the specific analysis API now ignore parameters not in the model.

This affects the _data_init_spin(), _sim_init_values_spin(), and _sim_return_param_spin() methods.
The result is that the spin containers no longer hold parameter variables set to None for non-model
parameters.

Merged revisions 19389-19397 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r19389 | bugman | 2013-04-05 18:04:35 +0200 (Fri, 05 Apr 2013) | 6 lines

The relaxation curve-fitting analysis parameters are now all lowercase.

This is to match the other analysis types so that the parameter names are identical to the
corresponding variable name. This is assumed by some of the specific analysis API methods.
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r19390 | bugman | 2013-04-05 18:08:42 +0200 (Fri, 05 Apr 2013) | 7 lines

Fix for the relaxation curve-fitting _assemble_scaling_matrix() method.

The intensity scaling was never activated before due to a lower vs. uppercase parameter name
mismatch. This scaling is now correctly set up as the previous code assumed cdp.relax_times was a
list whereas it has been a dictionary since the early 1.3 releases.
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r19391 | bugman | 2013-04-05 18:17:00 +0200 (Fri, 05 Apr 2013) | 6 lines

The grid search bounds for the relaxation curve-fitting are no longer affected by scaling.

The parameter scaling activated a few commits ago revealed a bug in the lower and upper data
structures for the grid search in that these were continuously scaled down.
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r19392 | bugman | 2013-04-05 18:23:30 +0200 (Fri, 05 Apr 2013) | 3 lines

Removal of junk code in the _assemble_scaling_matrix() relaxation curve-fitting method.
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r19393 | bugman | 2013-04-05 18:44:48 +0200 (Fri, 05 Apr 2013) | 5 lines

Parameter scaling is now functional in the target_function.relax_fit.c code.

Previously the scaling was not being used and the Python to C conversion was broken.
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r19394 | bugman | 2013-04-05 18:45:34 +0200 (Fri, 05 Apr 2013) | 3 lines

The scaling matrix is now converted into a usable list of diagonal elements for the relax_fit C module.
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r19395 | bugman | 2013-04-05 18:50:46 +0200 (Fri, 05 Apr 2013) | 3 lines

Fix for the target_functions.relax_fit C module - the scaling was incorrectly performed.
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r19396 | bugman | 2013-04-05 19:13:55 +0200 (Fri, 05 Apr 2013) | 3 lines

Simplified the code of the relax_fit C module.
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r19397 | bugman | 2013-04-05 19:28:34 +0200 (Fri, 05 Apr 2013) | 5 lines

Fix for the relaxation curve-fitting _back_calc() method for the changes to the C module.

The setup() method requires that the scaling matrix is converted to a list of the diagonal elements.
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Fix for the relaxation curve-fitting _back_calc() method for the changes to the C module.

The setup() method requires that the scaling matrix is converted to a list of the diagonal elements.

Simplified the code of the relax_fit C module.

Fix for the target_functions.relax_fit C module - the scaling was incorrectly performed.

The scaling matrix is now converted into a usable list of diagonal elements for the relax_fit C module.